Writing is a time-consuming process; writing high-quality publications requires attention to detail at every step of the way, from the actual prose on paper to its layout in the document to the presentation of figures. In this guide we walk you through 10 aspects of writing a scientific article using LaTeX to format your work. We emphasize typing commands at the unix command line in this guide as a way for you to peek under the hood of the LaTeX engine. This will allow you (the author!) power over the production of your own academic documents.

This guide could be extremely long. There are many, many fantastic resources on typesetting. Here we have hand-selected 10 topics to help lower the barrier to a more efficient and higher quality paper writing workflow. Specifically we focus on

  1. The structure of a document
  2. What are all of these tools? tex, latex, pdflatex, xelatex, lualatex, etc
  3. LaTeX happy workflows for your paper
  4. git and version control
  5. Journal style
  6. On writing, an interlude
  7. Dos and Don’ts
  8. On bibliographies
  9. On figures
  10. Handy tools

We provide a pile links to graphical interfaces to LaTeX at the end of the document, however emphasizing that value of

To help people practice these commands we have hands-on examples ready in a JupyterLab session, through Binder. Here you can follow along, processing documents in a terminal session. You can start this environment here.

To use LaTeX on your own computer, you will need to install it (we highly recommend following the links therein to TeX Live on each system).

1. Structure and Markup

A LaTeX document (or a .tex file) is a plain text document that contains commands that guides the LaTeX processing program how to create a beautiful pdf. These commands can be “markup” like \textbf{this is bold} for bold text or $\alpha + \beta \frac{1}{x^2}$ for math like \(\alpha + \beta \frac{1}{x^2}\) or commands that tell LaTeX about document structure like \section{Introduction} or even commands to identify a bibliography like \bibliography{refs_example.bib}.

Once you have a plain text document with markup, you then process it using a set of programs to create a publishable output like a .pdf file. This figure shows an example of a LaTeX document and highlights different parts of the document and their role.

The Structure of a LaTeX document

After processing that document (via, say, the command latexmk -pdflatex example.tex, assuming that the document is called example.tex), one can see a pdf file like the following image:

The associated pdf document

Takeaways

  • A LaTeX document is comprised of mainly two sections: preamble, which defines the styling, and the document text.
  • The LaTeX system separates concerns by allowing you to focus writing content in a plain text document, following by processing.
  • Processing the typed document delivers a layout that automatically handles spacing (as we will see later).

Practice

What does example.tex look like when compiled to a pdf document? Can you add a title or author? Can you make some text bold?1 You can practice by following these steps (and similar ones) later sections:

  1. select the directory 1_structure in the JupyterLab window that launches when you clink on launch binder from the readme.md file in the associated github repository
  2. Then clicking on the Terminal icon in the JupyterLab pane
  3. Once you are there, try typing latexmk -pdflatex example.tex and then looking at the pdf.

You can also copy the github repository to your own local machine and launch the Terminal to see a Unix command prompt if you are using a Mac or Linux machine. Windows machine also offer a unix command prompt, but it is a bit more involved to install it.

2. Flavors and Programs: tex, latex, pdflatex, etc

Although the most basic program that parses markup is called latex, in current daily use, you will mostly find yourself using pdflatex or even xelatex or maybe lualatex.

When Donald Knuth created this approach to making beautiful scientific documents, he started with the tex program but Leslie Lamport built latex by combining multiple tex commands into fewer and simpler macros. Both originally created documents in dvi or postscript format. Nowadays, pdf files are the best way to make a document that looks the same to all who want to view it on their screens or print it for themselves.

Here is a list of the common programs that one might use to create a pdf file from a latex document:

For example, at the command prompt in the Terminal, you might type pdflatex example.tex create an example.pdf file (if you only do it once, the citation will show up as a ? and no bibliography will be printed).

Notice also:

The following figure shows how it may require three runs of pdflatex (plus a run of bibtex) to go from an example.tex file to an example.pdf file:

From LaTeX to PDF commands

You can replace those multiple lines with a single call to latexmk -pdflatex example.tex.

Takeaways

  • Always use LaTeX markup: very rarely (if ever) should you need to dip into plain TeX
  • Always use PDF output (pdflatex) and PDF figures (or PNG … more on this later) rather than DVI or PS format for sharing generated documents

Practice

See the directory 2_texflavors and the readme.md file therein. Can you change the font and use xelatex to make a pdf, say, trying latexmk -xelatex example.tex?

3. LaTeX workflows

A given scientific paper will require many files and often involves many authors. For example, several .tex files (for different sections), multiple figures (in the form of .pdfs), and bibliographis (in .bib files) may all be part of the paper. Organizing these files is a consistent fashion will lead to a clear process when dealing with revisions at a later date.

As a specific example a main.tex file might look like this:

\documentclass{article}
\title{My Title}
\begin{document}
\maketitle
\input{abstract}
\input{intro}
\input{results}
...
\bibliography{mybib.bib}
\end{document}

But results.tex might look like this:

\section{Results}

Figure~\ref{fig:vaccine_by_pop} shows that opposition to vaccination peaks at a population of 100,000.

\begin{center}
\begin{figure}[!ht]
\includegraphics[width=.8\textwidth]{vaccine_by_pop.pdf}
\caption{Vaccination opposition by population}\label{fig:vaccine_by_pop}
\end{figure}
\end{center}

The number 100,000 and the figure vaccine_by_pop.pdf are derived from the R file called vaccine_by_pop.R. This R file relies on data that is cleaned by vaccine_data_cleaning.py, in addition to data that are downloaded, cleaned, and merged from the web.

So how do we organize the data, the files, and the overall workflow? There are many possibilities, but we’re reminded by a slice of the Zen of Python:

Simple is better than complex. Complex is better than complicated. Flat is better than nested.

We provide two specific examples of workflows below, first noting two aspects that will greatly improve your process. The first is to separate your data from your processing and presentation:

The second aspect, directly related to the LaTeX, is to establish a predictable naming convention. For example, each output like a table or figure uses one script with the same name:temp_vs_time.pdf <—> temp_vs_time.py and that LaTeX labelling follow this convention \label{fig:temp_vs_time}. When editing the document, the path from figure to the associated plotting script and related data is then clear.

On Directory Structure

Here are a two examples of directory structures have have worked for us:

In this example, we use Matt West’s directory structure, where the versions of the paper are kept in their own directories:

paper_topic_name_dir_name              | string used for repo, tex, and bib files
+ requirements.txt                     | number of pages,  etc
+ 1_submitted_paper
|   +-- paper_topic_name.tex
|   +-- refs_topic_name.bib
|   +-- journal_class.cls              | any files needed for the journal latex style
|   +-- figures
|   |   +-- temp_vs_time.pdf           | descriptive names for figures (not fig1.pdf, etc)
|   |   +-- error_vs_stepsize.pdf
|   |   `-- ...
|   +-- data                           | data files that generate the figures
|   |   +-- Makefile                   | Makefile that will re-generate all figures
|   |   +-- temp_vs_time.csv           | use the same name as the resulting figure
|   |   +-- plot_temp_vs_time.py       | plotting scripts, use names like plot_.py
|   |   `-- ...
|   `-- submitted_paper_topic_name.pdf | actual PDF file submitted
+ 2_reviews
|   +-- review_1.pdf                   | individual reviews
|   +-- review_2.pdf
|   `-- editor_statement.pdf           | instructions and summary from editor
+ 3_response_to_reviews
|   +-- response_topic_name.tex
|   `-- sent_response_topic_name.pdf   | actual PDF file sent to editor
` 4_revised_paper
    +-- paper_topic_name_revised.tex
    +-- refs_topic_name_revised.bib
    +-- journal_class.cls              | copy here any other files needed
    +-- figures                        | copy here all the figures again
    |   +-- temp_vs_time.pdf           | edit figures as needed
    |   +-- error_vs_stepsize.pdf
    |   `-- ...
    +-- data                           | copy all data again and edit as needed
    |   `-- ...
    `-- submitted_paper_topic_name_revised.pdf | actual PDF submitted

Reference: Matt West @ https://lagrange.mechse.illinois.edu/latex_quick_ref/

An alternative approach uses git branches for different versions, and a single Makefile for all tasks (from turning the paper into a pdf file via LaTeX, to creating figures, etc.). See also the discussion in Bowers and Voors (2016), section 3.

paper_topic_name_dir_name              | string used for repo, tex, and bib files
+ Makefile                             | file that tracks file relationships
+-- Data                               | directory for data and data cleaning, merging work
    + README.md                        | file with instructions and explanations
    + merge_data.R                     |
    + orig_data.csv                    | original data set, not to be changed
    + merge_data.csv                   |
    `-- ...                            |
+-- Analysis                           |
    + README.md                        |
    + linear_simulations.R             | file that runs simulations and saves output
    + linear_simulations.rda           | output from linear_simulations.R
    `-- ...                            |
+-- Figures                            |
    + README.md                        |
    + linear_simulations_N100.R        | file creating a figure
    + linear_simulations_N100.pdf      | the figure from linear_simulations_N100.R
    + descriptives.R                   | file creating a table
    + descriptives.tex                 | the table in LaTeX format
    `-- ...                            |
+-- Paper                              |
    + README.md                        |
    + main.tex                         | the main LaTeX file
    + abstract.tex                     | the abstract file
    `-- ...                            |
+-- References                         |
    + big.bib                          | bibliography file
    `-- ...                            |

Takeaways

  • Separate data from processing from presentation.
  • Create consistent labels in the LaTeX to script that generates it to the associated data.
  • Commit to a workflow! Anything is better than nothing and from the Zen of Python Now is better than never.

Practice

See the directory 3_workflows and the readme.md file therein.

4. On collaboration

Often your writing is often interleaved with edits and contributions from co-authors. How do you track changes and version in your LaTeX document?

Collaborating asychronously: git version control

We strongly recommend git version control via github, either when working along on a document or when multiple authors are involved. We do not git describe it in-depth here, but instead offer the following high-level best practices.

What files should you track (in version control)?

  • Your .tex file!
  • The .bib file for your article
  • Figures -> ./figures/*.pdf
  • Scripts for the figures -> ./data/*.py , ./data/*.R
  • Data for the figures -> ./data/*.csv
  • Any item you need to reproduce your paper that you cannot generate in your paper directory

What should you not track (in version control)?

  • Any data with personally identifying information or information that cannot ethically be made public.
  • The pdf of the paper -> paper_randnoise.pdf
  • Any typesetting output -> *.log, *.bbl, *.aux, etc
  • .DS_Store or other garbage from your system

Version control is invaluable as a collaboration tool, however it does require diligence when working with co-authors on a LaTeX document. We recommend the following recipe:

  • Agree with your co-authors on how you will organize the text in your documents. Specifically address expectations on
    • one sentence per line (of the LaTeX document)?
    • hard wrapping at say 80 characters?
    • nothing, free for all (plus or minus pre-commit automatic reformatting or checking of files)?
  • Commit changes often
  • For large edits, take specific sections at a time, to reduce merge conflicts
  • Before you commit and push, clean your LaTeX compile (latexmk myfile.tex -C) and recompile to verify there are no errors.
  • In the rare event when style files rely on a specific version, consider tracking the style file in your paper repository.

Collaborating synchronously

Fewer tools allow collaborators to edit plain text documents at the same time. We nearly always rely on asychronous collaboration, even if we have broken up a task and the whole team is working on it at the same time, even in the same room.

Overleaf is designed for this task. It compiles LaTeX and syncs with github. See also the online versions of LaTeX listed here.

There are other systems for editing plain text at the same time such as Teletype for Atom.

Takeaways

  • Agree on a tracking strategy with your collaborators
  • Do not add generated files such as log files to the repository
  • Do add files (such as figures, even though generated) in order to build the paper
  • Use the git for version control.

Practice

See the directory 4_git and the readme.md file therein.

5. Style

The overarching style of your document is often decided by the journal. With this in mind, it is best to typeset your document with the journal’s style file. The Society for Industrial and Applied Mathematics (SIAM) provides style files directly whereas others, e.g. American Mathematical Society journals, are included with your TeX distribution and available in CTAN. In any case, committing and not deviating from the expected format will accelerate your time-to-publication by not slowing down the copy editing at the journal. The style files will provide macros for author formats, custom figure environments, and almost certainly the preferred style for the bibilography. In addition, most journal provide a style guide that will detail the expectations on punctuation, hyphens, commas, etc.

Takeaways

  • Follow the journal style files and guides. It will save time.

Practice

See directory 5_style and readme.md for an example.

6. On Writing: An interlude…

You already know Hemingway’s famous quote: “the only kind of writing is re-writing”. However, you might not know about linters.

Linters?

A linter is a program that analyzes your text (sometimes in realtime, as you write it). When your mis-spelled words are highlighted in your email client, you are seeing the results of a linter alerting you to improve your text. Linters are also used in programming — catching code errors before running the code, by alerting you to unmatched parentheses or missing semi-colons.

Other linters can look for issues with style. Consider the following terrible sentence:

More research is needed to fill the gap created in extant literature in order to impact policy with very important findings.

One linter, the write-good, highlights several potential problems:

col 16 error| [write-good] "is needed" may be passive voice [E]
col 71 error| [write-good] "in order to" is wordy or unneeded [E]
col 102 error| [write-good] "very" is a weasel word and can weaken meaning [E]

Of course, linters cannot do it all. We use them because they draw attention to sentences that may need work. Ultimately they (hopefully) help focus our attention on prose: re-writing the sentence without using a passive voice, without using “impact” as a verb (!), and with a stronger justification for research than to just fill a gap in the literature.

Tips and Tricks

There are many fantastic tips and guides to improving your writing, from reading paragraphs and sentences out loud to “edit by ear” Becker (1986) to guides specific to academic writing: Gopen and Swan (1990) and Becker (1986). Here, we offer a few directions that improve your writing specifically in LaTeX:

  • Linters such as alex, proselint, and write-good can be integrated into many text editors (such as vim to highlight your .tex document on-the-fly.
  • In general, avoid the urge to constantly re-compile your document to view its output (figures/diagrams are a different case). Your first task is writing not reading.
  • Mark open items and second pass items with % TODO, a comment in the .tex file. You can find all places where you have % TODO in your document using: grep TODO paper_randnoise.tex
  • Outline. Write. Revise.
  • Polish and make it look visually appealing!

Takeaways

  • Peer reviewed publications are critically important to science
    • the quality of your presentation is important!
  • Peer reviewed publications take reviewer/editor time
    • the quality of your presentation is important!
  • (Hopefully) Many people will read your publication
    • the quality of your presentation is important!

Practice

See the directory 6_linting and the readme.md file therein.

7. LaTeX dos and don’ts

You will find that authors have their own macros, their own style in the .tex document, and they’re own preferences when using LaTeX. Here we offer general principles that can help improve your overall LaTeX workflow:

DO keep your LaTeX readable!

  • Block indent equations
\begin{align}
  \langle u, v \rangle & = \langle f, v\rangle\\
                       & = G(v)
\end{align}
  • Align tabular data
  \begin{tabular}{lrllr}
  \toprule
                 & \multicolumn{1}{c}{$n$}
                 & \multicolumn{1}{c}{$t$}
                 & \multicolumn{1}{c}{$\rho$}
                 & \multicolumn{1}{c}{$m$} \\
  \midrule
    experiment 1 & \num{    19929} & 0.32 & 0.8    & 55  \\
    experiment 2 & \num{  7729292} & 0.78 & 0.7    & 85  \\
    experiment 3 & \num{888173928} & 1.25 & 0.65   & 2   \\
  \bottomrule
  \end{tabular}
  • Limit whitespace in the .tex file

DON’T overuse macros

  • Macros are intended for complex arrangements with repeated use.
\newcommand{\Hcurl}{\vec{H}(\text{curl},\Omega)}
  • Macros are useful when notation might change that might change.
\renewcommand{\vec}[1]{\boldsymbol #1}
  • Macros are not shorthand; use them sparingly as others will find your .tex source unreadable.

DO use packages for consistent layouts

  • booktabs: provides clean horizontal lines for tables (avoid vertical lines), providing \toprule and \bottomrule in the example above.
  • siunitx: to format large numbers and notation, providing \num in the example above. High quality table

DON’T use \begin{align} for everything, instead try specific environments built for your purpose.

  • equation: base
  • align: multiple equations
  • split: one equation split with alignment
  • multline: one equation split with no alignment

DO use consistent fonts throughout (including within figures).

  • Label figures with
  • Label equations with
  • Label sections with
  • Label tables with

Takeaways

TODO

Practice

See the directory 7_dos and the readme.md file therein.

On citations and bibliographies

The LaTeX system allows you to (1) insert citations in your text using commands like \cite{ChOlSe_2021_lsrbm} which can turn into [7], (Chaudhry et al., 2021), [Ch21] or other citation styles within the text itself and also (2) to print out your bibliography, formatted according to your journal’s guidelines, using a single command in the LaTeX document like \bibliography{mybib.bib}. Separating formatting from information saves time: hundreds of citations will be printed automatically in the correct format if desired including only the sources you cited. If you decide that you no longer need a citation, this will be automatically removed from your bibliography. Journals often provide formatting guidelines in .bst files that can be referred to in the \bibliographystyle{} command.

The program bibtex (or biber) reads .aux files created by latex programs and creates a .bbl file which is then read by the latex program to format everything (above we showed the need to run latex, bibtex, latex, and latex in order for example, in order to make this work).

In order to use this system, you need a plain text file that is a database with entries formatted in BibTeX format. For example, here is one entry in the BibTeX file for this essay:

@article{ChOlSe_2021_lsrbm,
    author = {Chaudhry, Jehanzeb H. and Olson, Luke N. and Sentz, Peter},
    doi = {10.1137/20M1323552},
    journal = {SIAM Journal on Scientific Computing},
    number = {2},
    pages = {A1081-A1107},
    title = {A Least-Squares Finite Element Reduced Basis Method},
    url = {https://doi.org/10.1137/20M1323552},
    volume = {43},
    year = {2021}}

General workflow

The Structure of a LaTeX document with BIB

Takeaways

  • You will only need to add a BibTeX entry to your bibliography database (your .bib file) once. (And you can use tools like Zotero and BibDesk to make managing those collections of bibliographic information easier.)

Practice

See the directory 8_citations and the readme.md file therein.

On Figures and Tables and Math

Figures, tables, and math break up the text of a document and convey information that can make or break your attempts to persuade with your paper. We have a few suggestions about how to make these elements work with instead of against you here.

In general, if a figure or table has been created using code, your project should have a figure or table creation file like linear_simulations_N100.R which creates one figure in pdf format linear_simulations_N100.pdf. This figure creation file might require as input another file with simulation results, and in turn the simulation results creator file may need some data: we might notate this dependence among files like in our Makefile. For example in line 1 Data/clean_data.csv: Data/clean_data.R Data/raw_data.csv means that the file Data/clean_data.csv depends on Data/clean_data.R Data/raw_data.csv (is created by the .R file and the .csv file together). And line 2 is a command used to create Data/clean_data.csv (in this case, the command is R ---file Data/clean_data.R.

Data/clean_data.csv: Data/clean_data.R Data/raw_data.csv
    R ---file Data/clean_data.R

Analysis/linear_simulations.rda: Analysis/linear_simulations.R Data/clean_data.csv
    R --file Analysis/linear_simulations.R

Figures/linear_simulations_N100.pdf: Figures/linear_simulations_N100.R Analysis/linear_simulations.rda
    R --file Figures/linear_simulations_N100.R

In general Figures, Tables, and Math should appear close to where they are discussed in the text. Do not put them at the end of your document if you don’t want a grumpy reader: recall that most people are reading pdf documents on screens.

Figures

  • Tell LaTeX where to look for graphics using the \graphicspath{} command in the preamble. For example, we use \graphicspath{{.}{../Figures/}}.

  • We insert graphics into documents using the \includegraphics[]{} command. For example, if we wanted to include a figure but scale it to 1/3 of the width of the text (the area within the left and right margins), we would use: \includegraphics[width=0.3\textwidth]{myfig.pdf}.

  • Fonts in figures should match the fonts in the float/article. Note that using \includegraphics to scale a figure will also change the font sizes — be careful to ensure your figure text is easy to read.

  • You should attach a float environment after the paragraph of first reference. For example:

Figure~\ref{fig:vaccine_by_pop} shows that opposition to vaccination peaks at a population of 100,000.

\begin{center}
\begin{figure}[!ht]
\includegraphics[width=.8\textwidth]{vaccine_by_pop.pdf}
\caption{Vaccination opposition by population}\label{fig:vaccine_by_pop}
\end{figure}
\end{center}

  • Generally use \begin{figure}[!ht] or \begin{table}[!ht]

  • ! tex will ignore area restrictions

  • h place it “here” if it fits in the area

  • t place it at the “top” otherwise and if it fits otherwise create a new page

  • Don’t use \FloatBarrier and other tricks like \newpage, \vspace or \hspace for spacing

  • Use consistent color schemes in all figures throughout the paper.

  • Label everything. (TODO expand)

  • Do not introduce new notation in a figure or its caption. A reader should not have to hunt in the text to understand a figure.

  • The figure caption should describe, not discuss. A reader should not have to hunt in the text to understand a figure.

A terrible figure

Tables

  • If a table contains elements (like numbers) generated from code, then it should be generated entirely from code and saved in its own file.
    • In R, for example, we might use the xtable package to convert a matrix or data-frame to a LaTeX formatted table.
  • Tables should rarely have vertical lines, and in fact, tables should use as few lines as possible. (See this nice short guide on tables).

The figure caption should describe, not discuss. A reader should not have to hunt in the text to understand a figure.

Math

Math fonts should work with the main font of the article. For examples of good math and text font pairings see the LaTeX Font Catalogue.

Takeaways

TODO

Practice

See the directory 9_figures and the readme.md file therein.

Ways to type a document using LaTeX markup

A LaTeX document is a plain text file. This means that you can use any text editor to write a LaTeX document. However, a text editor that (1) recognizes that \textbf{} is a LaTeX command or that (2) keeps track of matching braces and parentheses makes it easier to write LaTeX markup. To that end, we use neovim (sometimes with the vimr gui) with vimtex plugins but we know that there are many other approaches to typing a plain text document using LaTeX markup.

Our friends who use LaTeX like the following systems. Each person prefers to interact with their computer differently, so we merely list what we’ve heard about here.

  • Emacs with Auctex
  • [Neovim or Vim with vimtex or texlab]
  • TexPad (we think this hides too many errors and warnings, so we think this is most useful so that you can go back to the command line)
  • TexShop (we think this hides too many errors and warnings, so we think this is most useful so that you can go back to the command line)
  • [TeXstudio]
  • [Atom]
  • [Sublime 3]

Journal Style (TEMPTED TO DROP THIS)

The journal will have a style file. For example, see: https://www.siam.org/publications/journals/about-siam-journals/information-for-authors#dnn_ctr2112_ContentPane

Following both of these will speed up the review and copy editing.

Practice

See the directory 5_style and the readme.md file therein.

Extra:

Helpful tools

Information about this document

We wrote this document using pandoc flavored markdown and turned it from plain text into HTML via the following command at the unix command line on our OS X laptops:

pandoc latex-guide.md --to html4 --from markdown+yaml_metadata_block+autolink_bare_uris+tex_math_single_backslash+inline_code_attributes --output latex-guide.html  --self-contained --variable bs3=TRUE --standalone --section-divs --template latex-guide-template.html   --include-in-header latex-guide-header.html --number-sections --table-of-contents --toc-depth=1  --variable theme=bootstrap --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --citeproc

Alternatively, if you have access to R, you can do the following to turn this markdown document into HTML.

Rscript -e "library(rmarkdown); render('latex-guide.md')"

References

Becker, Howard S. 1986. Writing for Social Scientists : How to Start and Finish Your Thesis, Book, or Article. University Of Chicago Press.
Bowers, Jake, and Maarten Voors. 2016. “Six Steps to a Better Relationship with Your Future Self, v 2.0.” Revista de Ciencia Polı́tica 36 (3): 829–48. http://static.jakebowers.org/PAPERS/11-BOWERS-RCP-363.pdf.
Gopen, George D, and Judith A Swan. 1990. “The Science of Scientific Writing.” American Scientist 78 (6): 550–58.

  1. Try out \title{Some Paper} and \author{Some Person} in the preamble and \maketitle just after the \begin{document} line.↩︎